[BioC] human miRNA predicted/validated targets

Ranjani R [guest] guest at bioconductor.org
Mon Jul 8 22:04:13 CEST 2013


Hi,
I am hoping to find an R package/downloadable resource for validated (and predicted) miRNA targets. I have already investigated a few sites : miRWalk (which is not downloadable in its entirety and has a limit on the number of miRNA you can feed into it's web form), tarBase (which does not seem to have been updated in a while) and miRecords. miRecords does have a downloadable excel spreadsheet with validated target information (and pubmed ID) - and has 2112 miRId -> Gene pairs.
Which is usually the methodology of choice for working with predicted/validated targets? I am concerned with using resources that may not be updated regularly -- or in downloading a file which may be a snapshot at a certain time.
Any guidance would be greatly appreciated.
Thanks,
Ranjani

 -- output of sessionInfo(): 

R version 2.15.2 (2012-10-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] VennDiagram_1.6.0  edgeR_3.0.8        limma_3.14.4       DESeq_1.10.1       lattice_0.20-15    locfit_1.5-9.1    
[7] Biobase_2.18.0     BiocGenerics_0.4.0

loaded via a namespace (and not attached):
 [1] annotate_1.36.0      AnnotationDbi_1.20.7 DBI_0.2-7            genefilter_1.40.0    geneplotter_1.36.0  
 [6] IRanges_1.16.6       parallel_2.15.2      RColorBrewer_1.0-5   RSQLite_0.11.4       splines_2.15.2      
[11] stats4_2.15.2        survival_2.37-4      tools_2.15.2         XML_3.98-1.1         xtable_1.7-1     

--
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